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9.6 years ago
benng60
•
0
I am using Pindel in the -i bam config mode. I am getting a lot of Inversions, and was wondering what is the best way to filter Pindel calls (in general)? I am converting Pindel to VCF using pindel2vcf.
Hi, have you known how to deal the pindel results?
It has been a while since I have used Pindel but I remember using variant quality threshold of 30 or higher to select high quality insertions and deletions. I have a script that works with Pindel output. For inversion, I filtered all the inversions that are less than 100 bp and variant quality of 30.
Hi Ashutosh, When I convert from Pindel to VCF, I do not get any quality scores, just Genotype and Allele depth. How do I get the variant quality threshold from this? Thank you.
Pindel also produces a big files with scores in it. This file also has the sequences that were used to call a particular variant. It will look like a multiple sequence alignment file. My script uses both the vcf file and the big file with scores as input and and annotates the vcf file.
Hi Ashutosh, I am a freshman, could you show a example to show me how to use your script? thanks a lot